Toe objective of this study is to verify the factors influencing the taxation cognition of medical institutions and to verify the difference of taxation cognition among the interest groups in medical services. The factors that influence taxation cognition are supposed to be five: cognition of public benefits on medical services, cognition of profits from medical institutions, cognition of self-responsibility of medical institutions, cognition of distinction of medical institutions, and cognition of the importance of medical services. The interest groups are divided into four: medical institution employees, medical treatment consumers, taxation experts, and tax officials. As a result of this study, first, cognition of public benefits, cognition of profits, and cognition of distinction are verified to have statistical significance as factors for taxation cognition. It means that cognition of the public benefits of medical services is low, while cognition of profits is high, and taxation cognition such as tax supports and tax exemption appears low in accordance with lowness of cognition of distinction of medical institutions. Second, taxation cognition of the interest groups about medical service shows statistical significance between the group of medical institution employees and the group of tax officials, and between the group of medical institution employees and the group of taxes experts. This study is expected to contribute to tax policy, which can support medical institutions to provide medical consumers with good medical services, by analyzing the factors that influence taxation cognition on medical institutions.